Align TRAP dicarboxylate transporter, DctP subunit (characterized, see rationale)
to candidate Echvi_3629 Echvi_3629 tripartite ATP-independent periplasmic transporter solute receptor, DctP family
Query= uniprot:Q88NN8 (323 letters) >FitnessBrowser__Cola:Echvi_3629 Length = 335 Score = 215 bits (547), Expect = 1e-60 Identities = 113/318 (35%), Positives = 189/318 (59%), Gaps = 3/318 (0%) Query: 7 LLLAVLPFAFSVAMPASALDIKFAEIHPAGYPTVVAEQNMGKKLEDASNGEITFKMFAGG 66 LL +L +FS P S IK +P A M K+LE+ S+G++T K++ Sbjct: 17 LLFGLLVVSFSCQGPGSKRVIKLGHGLDTKHPVHEAMLYMAKRLEEKSDGKLTMKVYPNA 76 Query: 67 VLGSEKEVIEQAQIGAVQMTRVSLGIVGPVVPDVNVFNMPFVFRDHDHMRKIIDGEIGQE 126 LG+E+E++E QIG++ MT+VS ++ P + V + P++FRD+ H ++++GEIG+ Sbjct: 77 QLGNERELVELLQIGSLGMTKVSSAVMESFAPKIQVLSQPYLFRDNGHRERVLNGEIGKR 136 Query: 127 ILDKITNSDFNLVALAWMDGGSRSIYTK-KPVRSLEDLKGMKIRVQGNPLFIDMMNAMGG 185 +L++ T F L L + D GSRS YTK KPV S EDL G KIRV + I+M+N+ GG Sbjct: 137 LLNEGTQ--FWLKGLCFYDAGSRSFYTKDKPVESPEDLVGKKIRVMESNTAINMVNSFGG 194 Query: 186 NGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHFQSAKYYTLTGHLILPEPVVMSKTTW 245 + + GE+++ALQ G++DGAENNPP+++ H++ K+Y+L H +P+ +++S W Sbjct: 195 SPTPVSWGELYTALQQGIVDGAENNPPSVISSRHYEICKFYSLDEHTAVPDMLIVSTKVW 254 Query: 246 NKLSPEQQALVKKVAREAQMEERALWDAKSAASEEKLKAAGVEFITVDKKPFYDATASVR 305 ++LS E+Q +++ A E+ + +W S +L+A GV DK+PF A + Sbjct: 255 DRLSEEEQNWLQEAADESAKFQYKIWAEAEEESMRQLEAEGVTITRPDKEPFRKAVEPMY 314 Query: 306 EKYGAQYADLMKRIDAVQ 323 E+ ++ + I+ ++ Sbjct: 315 EQIKQSQPEMYEIIEKIR 332 Lambda K H 0.318 0.134 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 249 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 323 Length of database: 335 Length adjustment: 28 Effective length of query: 295 Effective length of database: 307 Effective search space: 90565 Effective search space used: 90565 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory